The mouse brain comprises ~70 million neurons and ~30 million glia and other cells. Neurons have been traditionally classified based on their morphology, connectivity, stimulus-response, gene expression, and location in the brain. While we know reasonably well the main cell types that are present at different brain locations, we have little quantitative knowledge about brainwide cell type distribution. In addition, cell type-based brainwide connectivity, especially at the level of projection patterns of single neurons, also remains largely unmapped. This knowledge gap prevents us from incorporating the accumulated cell type-based cellular data into comprehensive circuit models of mammalian brain function. Here we propose to develop a largely automated methodology for 1) quantitative atlasing of neuronal and glia cell types on the basis of their complete cell counts per anatomical regions in the whole mouse brain, and 2) complete tracing of axonal arborizations of identified neuronal cell types. The specific Aims are: Specific Aim 1 (FOA goals 1, 4-6): To develop a versatile platform for brainwide atlasing of molecularly defined cell types. Computational and statistical methods will be developed to obtain accurate cell numbers in whole brains of cell type-specific reporter mice imaged by serial two-photon (STP) tomography and registered to reference brain atlases. These methods will then be used to map the distribution of five different GABAergic cell types during development, in the adult male and female brain, and during aging. Specific Aim 2 (FOA goal 6): To enhance the throughput of cell type-based atlasing and connectivity mapping through the development of a second-generation imaging platform. A light-sheet fluorescent microscopy-based method, named Oblique Plane Tomography (OPT), will be developed for fast high- resolution imaging of CLARITY-treated mouse brains. Computational methods will be established to allow the use of OPT in cell type atlasing and projection tracing in the whole mouse brain. Specific Aim 3 (FOA goals 2-3): Neuroinformatics infrastructure: an integrated web portal for cell-type specific data, tools & analytics. The developed methods, including a statistical toolbox for online and offline analytics, and the data generated will be distributed via a public website that will also serve to integrate the relevant information on the molecular identity, location, connectivity and other cell type characteristics. Relevance to public health: We will establish an automated and quantitative approach to the study of cell type distribution and connectivity in the mouse brain. Our methods can be readily scaled up and applied to a broad range of cell type-specific studies of both normal brain functions and pathological conditions related to human brain disorders.